Coding

Part:BBa_K1159314

Designed by: Dong-Jiunn Jeffery TRUONG   Group: iGEM13_TU-Munich   (2013-09-16)

TMD with N-terminal Signal Peptide of SERK Receptor from ''P. patens'' in RFC[25] N-Part

This part codes for the Transmembrane Domain with N-terminal Signal Peptide of SERK Receptor from P. patens in RFC[25]. This construct is flanked by RFC[25] N-part prefix and suffix. Note: This means only protein fusions to the C-terminus of this part is possible, adding promoters (typically RFC[10]) into the prefix or terminators/IRES (typically RFC[10]) into the suffix of this part is nevertheless possible.

Sequence and Features

Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 25 N-Part using the stop codon in the suffix, so ACCGGT was added (in italics) to the 3' end: (underlined part encodes the protein)
 AACAATGCCTGGT ... ATTGAGGCTACCGGT
 ORF from nucleotide position 5 to 298 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
MPGEVAWWRPLFLIALMPIGVLSNAEGDALNTTGPGQPPFPPPPPFTPPPPQTPNGASGENSTGAIAGGVAAGAALLFAAPAIGFAWWRRRRPIEATG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
RFC25 scar (shown in bold): 33 to 34
Amino acid composition:
Ala (A)16 (16.3%)
Arg (R)5 (5.1%)
Asn (N)4 (4.1%)
Asp (D)1 (1.0%)
Cys (C)0 (0.0%)
Gln (Q)2 (2.0%)
Glu (E)4 (4.1%)
Gly (G)13 (13.3%)
His (H)0 (0.0%)
Ile (I)5 (5.1%)
Leu (L)7 (7.1%)
Lys (K)0 (0.0%)
Met (M)2 (2.0%)
Phe (F)5 (5.1%)
Pro (P)18 (18.4%)
Ser (S)3 (3.1%)
Thr (T)6 (6.1%)
Trp (W)4 (4.1%)
Tyr (Y)0 (0.0%)
Val (V)3 (3.1%)
Amino acid counting
Total number:98
Positively charged (Arg+Lys):5 (5.1%)
Negatively charged (Asp+Glu):5 (5.1%)
Aromatic (Phe+His+Try+Tyr):9 (9.2%)
Biochemical parameters
Atomic composition:C463H699N123O124S2
Molecular mass [Da]:10036.5
Theoretical pI:6.07
Extinction coefficient at 280 nm [M-1 cm-1]:22000 / 22000 (all Cys red/ox)
Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges 
Codon usage
Organism:E. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
Codon quality (CAI):good (0.70)good (0.72)good (0.77)excellent (0.92)excellent (0.90)good (0.75)
Alignments (obtained from PredictProtein.org)
SwissProt:Q94F62 (65% identity on 20 AAs), Q9SKG5 (45% identity on 67 AAs)
TrEML:A9RY79 (80% identity on 81 AAs), B9FZB8 (77% identity on 36 AAs)
PDB: -
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:secreted (63%)
Bacteria:secreted (45%)
Eukarya:mitochondriamembrane (41%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology: -
 
Predicted features:
Disulfid bridges: -
Transmembrane helices:67 to 84 going inwards
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[edit]
Categories
//chassis/eukaryote/ppatens
Parameters
None